{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,7]],"date-time":"2026-10-07T08:53:09Z","timestamp":1791363189669,"version":"4.3.1"},"reference-count":22,"publisher":"Springer Science and Business Media LLC","issue":"10","license":[{"start":{"date-parts":[[2026,9,22]],"date-time":"2026-09-22T00:00:00Z","timestamp":1790035200000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0"},{"start":{"date-parts":[[2026,9,22]],"date-time":"2026-09-22T00:00:00Z","timestamp":1790035200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0"}],"funder":[{"DOI":"10.13039\/100000002","name":"U.S. Department of Health & Human Services | National Institutes of Health","doi-asserted-by":"publisher","award":["R56HG012310"],"award-info":[{"award-number":["R56HG012310"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"U.S. Department of Health & Human Services | National Institutes of Health","doi-asserted-by":"publisher","award":["R01CA287673"],"award-info":[{"award-number":["R01CA287673"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"U.S. Department of Health & Human Services | National Institutes of Health","doi-asserted-by":"publisher","award":["R01HD114705"],"award-info":[{"award-number":["R01HD114705"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"U.S. Department of Health & Human Services | National Institutes of Health","doi-asserted-by":"publisher","award":["U54NS115198"],"award-info":[{"award-number":["U54NS115198"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"U.S. Department of Health & Human Services | National Institutes of Health","doi-asserted-by":"publisher","award":["R35GM134863"],"award-info":[{"award-number":["R35GM134863"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"U.S. Department of Health & Human Services | National Institutes of Health","doi-asserted-by":"publisher","award":["R35GM158057"],"award-info":[{"award-number":["R35GM158057"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Mitochondrial Medicine Frontier Program"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Nat Methods"],"published-print":{"date-parts":[[2026,10]]},"DOI":"10.1038\/s41592-026-03225-4","type":"journal-article","created":{"date-parts":[[2026,9,22]],"date-time":"2026-09-22T09:03:29Z","timestamp":1790067809000},"page":"1968-1972","update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["NanoTS: a deep learning tool for accurate SNP calling in nanopore long-read transcriptome data"],"prefix":"10.1038","volume":"23","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-3516-3999","authenticated-orcid":false,"given":"Zelin","family":"Liu","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8346-4692","authenticated-orcid":false,"given":"Feng","family":"Wang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2614-5956","authenticated-orcid":false,"given":"Robert","family":"Wang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6197-7091","authenticated-orcid":false,"given":"David W.","family":"Wu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nicole","family":"DeBruyne","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7451-5117","authenticated-orcid":false,"given":"Kelsey","family":"Keith","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Elizabeth M.","family":"McCormick","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0004-4298-595X","authenticated-orcid":false,"given":"Joseph Jee-Hwan","family":"Park","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Matthew T.","family":"Sullenberger","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0313-0743","authenticated-orcid":false,"given":"Andrew C.","family":"Edmondson","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1723-6728","authenticated-orcid":false,"given":"Marni J.","family":"Falk","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9905-8928","authenticated-orcid":false,"given":"Lan","family":"Lin","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9257-7613","authenticated-orcid":false,"given":"Yi","family":"Xing","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2026,9,22]]},"reference":[{"key":"3225_CR1","doi-asserted-by":"publisher","first-page":"883","DOI":"10.1016\/j.ymthe.2024.11.025","volume":"33","author":"IH Ament","year":"2025","unstructured":"Ament, I. H., DeBruyne, N., Wang, F. & Lin, L. Long-read RNA sequencing: a transformative technology for exploring transcriptome complexity in human diseases. Mol. Ther. 33, 883\u2013894 (2025).","journal-title":"Mol. Ther."},{"key":"3225_CR2","doi-asserted-by":"publisher","first-page":"641","DOI":"10.1016\/j.ajhg.2013.08.008","volume":"93","author":"R Piskol","year":"2013","unstructured":"Piskol, R., Ramaswami, G. & Li, J. B. Reliable identification of genomic variants from RNA-seq data. Am. J. Hum. Genet. 93, 641\u2013651 (2013).","journal-title":"Am. J. Hum. Genet."},{"key":"3225_CR3","doi-asserted-by":"publisher","first-page":"803","DOI":"10.1038\/s41587-023-01873-x","volume":"42","author":"J Dou","year":"2024","unstructured":"Dou, J. et al. Single-nucleotide variant calling in single-cell sequencing data with Monopogen. Nat. Biotechnol. 42, 803\u2013812 (2024).","journal-title":"Nat. Biotechnol."},{"key":"3225_CR4","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-023-02923-y","volume":"24","author":"VBC De Souza","year":"2023","unstructured":"De Souza, V. B. C. et al. Transformation of alignment files improves performance of variant callers for long-read RNA sequencing data. Genome Biol. 24, 91 (2023).","journal-title":"Genome Biol."},{"key":"3225_CR5","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-025-67237-y","volume":"16","author":"Z Zheng","year":"2025","unstructured":"Zheng, Z. et al. Clair3-RNA: a deep learning-based small variant caller for long-read RNA sequencing data. Nat. Commun. 16, 11553 (2025).","journal-title":"Nat. Commun."},{"key":"3225_CR6","doi-asserted-by":"publisher","DOI":"10.1038\/s41592-026-03045-6","author":"N Huang","year":"2026","unstructured":"Huang, N. et al. SNP calling, haplotype phasing and allele-specific analysis with long RNA-seq reads. Nat. Methods https:\/\/doi.org\/10.1038\/s41592-026-03045-6 (2026).","journal-title":"Nat. Methods"},{"key":"3225_CR7","doi-asserted-by":"publisher","first-page":"246","DOI":"10.1038\/nbt.2835","volume":"32","author":"JM Zook","year":"2014","unstructured":"Zook, J. M. et al. Integrating human sequence data sets provides a resource of benchmark SNP and indel genotype calls. Nat. Biotechnol. 32, 246\u2013251 (2014).","journal-title":"Nat. Biotechnol."},{"key":"3225_CR8","doi-asserted-by":"publisher","unstructured":"Martin, M. et al. WhatsHap: fast and accurate read-based phasing. Preprint at bioRxiv https:\/\/doi.org\/10.1101\/085050 (2016).","DOI":"10.1101\/085050"},{"key":"3225_CR9","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-023-40083-6","volume":"14","author":"F Wang","year":"2023","unstructured":"Wang, F. et al. TEQUILA-seq: a versatile and low-cost method for targeted long-read RNA sequencing. Nat. Commun. 14, 4760 (2023).","journal-title":"Nat. Commun."},{"key":"3225_CR10","doi-asserted-by":"publisher","first-page":"801","DOI":"10.1038\/s41592-025-02623-4","volume":"22","author":"Y Chen","year":"2025","unstructured":"Chen, Y. et al. A systematic benchmark of Nanopore long-read RNA sequencing for transcript-level analysis in human cell lines. Nat. Methods 22, 801\u2013812 (2025).","journal-title":"Nat. Methods"},{"key":"3225_CR11","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-019-11272-z","volume":"10","author":"C Soneson","year":"2019","unstructured":"Soneson, C. et al. A comprehensive examination of Nanopore native RNA sequencing for characterization of complex transcriptomes. Nat. Commun. 10, 3359 (2019).","journal-title":"Nat. Commun."},{"key":"3225_CR12","doi-asserted-by":"publisher","first-page":"435","DOI":"10.1038\/nrg1348","volume":"5","author":"H Ellegren","year":"2004","unstructured":"Ellegren, H. Microsatellites: simple sequences with complex evolution. Nat. Rev. Genet. 5, 435\u2013445 (2004).","journal-title":"Nat. Rev. Genet."},{"key":"3225_CR13","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-024-51252-6","volume":"15","author":"A Byrne","year":"2024","unstructured":"Byrne, A. et al. Single-cell long-read targeted sequencing reveals transcriptional variation in ovarian cancer. Nat. Commun. 15, 6916 (2024).","journal-title":"Nat. Commun."},{"key":"3225_CR14","unstructured":"Lefeber, D. J., Freeze, H. H., Steet, R. & Kinoshita, T. Congenital disorders of glycosylation. In Essentials of Glycobiology (eds. Varki, A. et al.) Ch. 45 (Cold Spring Harbor Laboratory Press, 2022)."},{"key":"3225_CR15","doi-asserted-by":"publisher","DOI":"10.1038\/nrdp.2016.80","volume":"2","author":"GS Gorman","year":"2016","unstructured":"Gorman, G. S. et al. Mitochondrial diseases. Nat. Rev. Dis. Primer 2, 16080 (2016).","journal-title":"Nat. Rev. Dis. Primer"},{"key":"3225_CR16","doi-asserted-by":"publisher","first-page":"543","DOI":"10.1002\/(SICI)1098-1004(199912)14:6<543::AID-HUMU17>3.0.CO;2-S","volume":"14","author":"S Vuillaumier-Barrot","year":"1999","unstructured":"Vuillaumier-Barrot, S. et al. Characterization of the 415G>A (E139K) PMM2 mutation in carbohydrate-deficient glycoprotein syndrome type Ia disrupting a splicing enhancer resulting in exon 5 skipping. Hum. Mutat. 14, 543\u2013544 (1999).","journal-title":"Hum. Mutat."},{"key":"3225_CR17","doi-asserted-by":"publisher","first-page":"535","DOI":"10.1016\/j.cell.2018.12.015","volume":"176","author":"K Jaganathan","year":"2019","unstructured":"Jaganathan, K. et al. Predicting splicing from primary sequence with deep learning. Cell 176, 535\u2013548.e24 (2019).","journal-title":"Cell"},{"key":"3225_CR18","doi-asserted-by":"publisher","first-page":"3094","DOI":"10.1093\/bioinformatics\/bty191","volume":"34","author":"H Li","year":"2018","unstructured":"Li, H. Minimap2: pairwise alignment for nucleotide sequences. Bioinformatics 34, 3094\u20133100 (2018).","journal-title":"Bioinformatics"},{"key":"3225_CR19","doi-asserted-by":"crossref","unstructured":"Garrido-Mart\u00edn, D., Palumbo, E., Guig\u00f3, R. & Breschi, A. ggsashimi: Sashimi plot revised for browser- and annotation-independent splicing visualization. PLoS Comput. Biol. 14, e1006360 (2018).","DOI":"10.1371\/journal.pcbi.1006360"},{"key":"3225_CR20","doi-asserted-by":"publisher","first-page":"24","DOI":"10.1038\/nbt.1754","volume":"29","author":"JT Robinson","year":"2011","unstructured":"Robinson, J. T. et al. Integrative genomics viewer. Nat. Biotechnol. 29, 24\u201326 (2011).","journal-title":"Nat. Biotechnol."},{"key":"3225_CR21","doi-asserted-by":"publisher","first-page":"D925","DOI":"10.1093\/nar\/gkae977","volume":"53","author":"L Phan","year":"2025","unstructured":"Phan, L. et al. The evolution of dbSNP: 25 years of impact in genomic research. Nucleic Acids Res. 53, D925\u2013D931 (2025).","journal-title":"Nucleic Acids Res."},{"key":"3225_CR22","doi-asserted-by":"publisher","unstructured":"Liu, Z. NanoTS: a deep learning tool for accurate SNP calling in nanopore long-read transcriptome data. Zenodo https:\/\/doi.org\/10.5281\/zenodo.19900024 (2026).","DOI":"10.5281\/zenodo.19900024"}],"container-title":["Nature Methods"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.nature.com\/articles\/s41592-026-03225-4.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s41592-026-03225-4","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s41592-026-03225-4.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,10,7]],"date-time":"2026-10-07T08:33:59Z","timestamp":1791362039000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.nature.com\/articles\/s41592-026-03225-4"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,9,22]]},"references-count":22,"journal-issue":{"issue":"10","published-print":{"date-parts":[[2026,10]]}},"alternative-id":["3225"],"URL":"https:\/\/doi.org\/10.1038\/s41592-026-03225-4","relation":{},"ISSN":["1548-7091","1548-7105"],"issn-type":[{"value":"1548-7091","type":"print"},{"value":"1548-7105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,9,22]]},"assertion":[{"value":"18 August 2025","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"13 August 2026","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"22 September 2026","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"L.L., Y.X. and F.W. are inventors on a patent application filed by The Children\u2019s Hospital of Philadelphia covering the TEQUILA method (US Patent 63\/277,894). The other authors declare no competing interests.","order":1,"name":"Ethics","label":"Competing interests","group":{"name":"EthicsHeading","label":"Ethics"}}]}}